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Physics LibreTexts

Transient Photobiology

Transient Photobiology is the study of interactions between light and biological systems over a set time scale. A range of behaviors at a variety of timescales can be examined, including timescales in the femtosecond range. 

Ultrafast Optics

Ultrafast optics refers to the use of extremely brief laser pulses—typically with a duration in the femtosecond (10-15 seconds) or picosecond (10-12 seconds) range—to observe events occurring over extremely short timescales. The technique is analogous to the use of stop-motion photography to record images of fast-moving objects, such as a hummingbird’s wings—that cannot be resolved at  standard timescales.

Sources: User:Mdf (Wikipedia) and "Good-e-nuf" (Deviantart)

Figure 1: A hummingbird's wings at two different time resolutions, illustrating the value of high-speed imaging techniques.

Photo 1 by "User:Mdf", distributed under GNU Free Documentation License Source 1

Photo 2 by Walt "Good-e-nuf", distributed under CC Source 2


While the aforementioned hummingbird flaps its wings once every 1/50 seconds, chemical bond formations have timescales on the order of femtoseconds. This necessitates the use of ultrafast optical techniques, as this timescale is beyond the reach of contemporary electronic equipment (contemporary CPU and RAM clock cycles occur at the nanosecond time scale).


Lasers produce amplified light through the process of stimulated emission, in which an intense energy source (known as the “pump”) is used to excite a large number of electrons in the laser medium, such that there are more excited electrons in the medium than ground state electrons. As incident photons pass through these excited atoms, the excited electrons quickly drop to the ground state, emitting photons of similar wavelength in a process known as stimulated emission.


Source: V1adis1av (Wikipedia)



Figure 2: Diagram illustrating the process of stimulated emission--through which a transient photon causes an excited electron to emit a photon of equal wavelength. 

Figure by "V1adis1av", distributed under GNU Free Documentation License Source




Mirrors are placed on both ends of the laser medium, causing the emitted light to repeatedly reflect back and forth. This has the effect of causing the light in this “amplification chamber” to eventually be filtered out to a single wavelength, as photons of errant wavelengths will not strike the mirrors at perpendicular angles—causing them to eventually ricochet out of the chamber. The remaining photons will eventually stream out through the partial mirror on one side of the amplification chamber.


Figure 3: Video describing the amplification and stimulated emission components of laser generation[5][6]. Video distributed under CC Source Source 2

Setting up Ultrashort Pulses

In order to generate a light pulse with a short enough timescale, it is necessary to “phase lock” the light waves produced by the laser—that is, align the crests of the waves to maximize the area of the wave over which destructive interference occurs, while simultaneously maximizing local constructive interference at a single point on the wave. 

Source: Arnd Krueger and Philippe Féru, SPIE



Figure 4: Diagram illustrating the importance of phase-locking when producing ultrashort laser pulses. Random phase light stretches the timescale over which the sample is exposed to the radiation. In this phase-locked sample, the heavily-concentrated constructive interference causes the sample to receive the entire wave packet in a very short amount of time[8].





The phases don’t tend to stay locked, however. Longer wavelengths tend to have higher group velocities than shorter ones, which tends stretch out the laser pulse as it transitions through different media—such as air or glass—leading to differential bending of the component wavelengths of the pulse.

It is possible to recompress a chirped pulse with a proper arrangement of prisms. If the prisms in such a “pulse compressor” are arranged such that the longer wavelengths in the chirped pulse travel through more glass before entering the air again, the pulse can be compressed back into an ultrashort, phase-locked pulse.

Source: Dr. Delmar Larsen (2/17/2015)


Figure 5: Diagram depicting a "pulse compressor" setup consisting of an array of prisms aligned in such a way as to lengthen the path of the shorter wavelengths in a "chirped" pulse, with the aim of bringing the wave-packet back in phase.

Figure by Han-Kwang Nienhuys, under GNU Free Distribution License Source

Pump-Probe Technique

Pump-probe technique is the simplest ultrafast spectroscopy method currently in use. First, a high-energy "pump" laser pulse is used to excite the atoms or molecules in a sample. A second, weaker, pulse is then used to measure the effect of the first pulse on the particles in the sample. By repeating this process with differing time gaps between the first and second pulses, a frame-by-frame view of the sample can be recorded—enabling the progression of chemical reactions to be observed with femtosecond time resolution.

Figure 6: Video describing how Pump-Probe Technique utilizes two laser pulses to measure a sample, along with sample applications of the technique[5][7]. Video distributed under CC Source Source 2


As previously mentioned, ultrashort pulses can be used in experiments requiring extremely fast instrumentation—such as the observation of chemical bond formation or conformational changes in larger molecules. Additionally, the impact light has on the behavior of electrons can be used to influence to outcome of said reactions if timed correctly.  

Photosensitive Proteins

Many proteins, such as Rhodopsin, undergo conformational changes upon exposure to photons of the proper frequency. One component of this conformational change is the photoisomerization of retinal—in which 11-cis retinal isomerizes to all-trans retinal. By using pump-probe spectroscopy to construct a time-lapse of the reaction, it has been determined that this isomerization process occurs in approximately 200 femtoseconds, and persists for around three picoseconds before reverting back to the 11-cis form[4].

Influencing Chemical Reactions

Ultrashort laser pulses with the correct phase and amplitude can be used to control the outcome of chemical reactions, by bombarding molecules with laser pulses resonant with electronic transitions. This alters the chemical potential energy of the system, which can lead to the formation of different products than would have formed from the ground-state system. Where ultrafast pulses go above and beyond the capabilities of standard photochemistry is with the direct, selective cleavage of chemical bonds[2]—with femtosecond timsecale laser pulses, it is theoretically possible to beat the timescale of intramolecular vibrational energy redistribution (IVR) and achieve direct, selective control of chemical reactions[3].


1.) Larsen, Delmar. Lecture Content. 17 Feb. 2015.

2.) Levis, R. J. "Selective Bond Dissociation and Rearrangement with Optimally Tailored, Strong-Field Laser       Pulses." Science (2001): 709-13. Web. 19 Mar. 2015. <>.

3.) Lozovoy, Vadim V., Yair Andegeko, Xin Zhu, and Marcos Dantus. "Applications of Ultrashort Shaped Pulses in Microscopy and for       Controlling Chemical Reactions." Chemical Physics: 118-24. Web. 3 Mar. 2015.                                                                                               <>.

4.) Yan, Ming, Louis Rothberg, and Robert Callender. "Femtosecond Dynamics of Rhodopsin Photochemistry Probed by a Double           Pump Spectroscopic Approach." The Journal of Physical Chemistry B: 856-59. Web. 19 Mar. 2015.                                                             <>.

5.) J. Bobroff. University of Paris-Sud. "Tout Est Quantique." Quantum Made Simple. Web. 3 Mar. 2015.       <>.

6.) J. Bobroff. University of Paris-Sud. "Tout Est Quantique." Quantum Made Simple. Web. 3 Mar. 2015.                                                            <​>.

7.) J. Bobroff. University of Paris-Sud. "Tout Est Quantique." Quantum Made Simple. Web. 3 Mar. 2015.                                                 <>.

8.) SPIE. "Lasers & Sources." Getting Practical. Web. 19 Mar. 2015. <>.